Genomics, computation and sequencing

Mortazavi Lab at UC Irvine

Research

There are many diverse projects going on in the lab

Long-read Transcriptomics

We are leveraging the PacBio and Oxford Nanopore platforms to sequence full-length transcripts in order to characterize the true extent of alternative splicing. We are both sequencing transcriptomes as well as developing tools to enable these analyses.

IGVF

We are leveraging mouse genetic diversity to study the impact of genotype on molecular function in a variety of tissues at single-cell resolution.

Model AD

We are part of a NIA Consortium to build better late-onset Alzheimer’s Disease models in mouse. Our part includes both bioinformatics as well as single-cell transcriptomics in these new models.

FSHD

We are using functional genomics to understand the mechanisms driving the pathology of Facioscapulohumeral muscular dystrophy using single-cell and single-nucleus techniques.

Gene Regulatory Networks

We are building models of gene regulatory networks using either bulk or single-cell RNA-seq, and ATAC-seq in human, rodents, and other vertebrates in order to discover how the logic of development is encoded in the genome.

Cellular Differentiation

We study myogenesis and macrophage differentiation using functional genomics assays such RNA-seq, microRNA-seq, ATAC-seq, and ChIP-seq in order to understand how gene expression and chromatin states change in time courses of differentiation.

Software

Software produced by the lab used to analyze genomics data

Topyfic

Reproducible latent dirichlet allocation (LDA) for single cell epigenomics data

Cerberus

Triplet-based transcriptome harmonization and diversity

PyWGCNA

Weighted Gene Correlation Network Analysis

Lapa

Alternative polyadenylation detection

Swan

Transcriptome analysis and visualization

TALON

Long-read RNA-seq annotator

TranscriptClean

Long-read RNA-seq error correction

SOMatic

High-dimensional data clustering with SOMs

People

Ali Mortazavi, PhD

Principal Investigator

Elisabeth Rebboah

MCSB PhD Student

Fairlie Reese, PhD

Postdoctoral fellow

Heidi Liang

Lab Technician / Sequencing Specialist

Jasmine Sakr

Pharmaceutical Sciences PhD Student

Narges Rezaie

MCSB PhD Student

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